메뉴 건너뛰기




Volumn 87, Issue 3, 2014, Pages 576-585

Monitoring the rumen pectinolytic bacteria Treponema saccharophilum using real-time PCR

Author keywords

16S rRNA gene; Forage; Pectin; Treponema saccharophilum

Indexed keywords

ABUNDANCE; ALFALFA; BACTERIOLOGY; BACTERIUM; HAY; POLYMERASE CHAIN REACTION; POLYSACCHARIDE; POPULATION DENSITY; REAL TIME;

EID: 84896712131     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12246     Document Type: Article
Times cited : (40)

References (53)
  • 1
    • 29144445330 scopus 로고    scopus 로고
    • PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample
    • Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V & Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71: 8966-8969.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8966-8969
    • Acinas, S.G.1    Sarma-Rupavtarm, R.2    Klepac-Ceraj, V.3    Polz, M.F.4
  • 3
    • 77749334332 scopus 로고    scopus 로고
    • Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis
    • Bekele AZ, Koike S & Kobayashi Y (2010) Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis. FEMS Microbiol Lett 305: 49-57.
    • (2010) FEMS Microbiol Lett , vol.305 , pp. 49-57
    • Bekele, A.Z.1    Koike, S.2    Kobayashi, Y.3
  • 4
    • 79551500179 scopus 로고    scopus 로고
    • Phylogenetic diversity and dietary association of rumen Treponema revealed using group-specific 16S rRNA gene-based analysis
    • Bekele AZ, Koike S & Kobayashi Y (2011) Phylogenetic diversity and dietary association of rumen Treponema revealed using group-specific 16S rRNA gene-based analysis. FEMS Microbiol Lett 316: 51-60.
    • (2011) FEMS Microbiol Lett , vol.316 , pp. 51-60
    • Bekele, A.Z.1    Koike, S.2    Kobayashi, Y.3
  • 5
    • 0013628771 scopus 로고
    • Characteristics of two new genera of anaerobic curved rods isolated from the rumen of cattle
    • Bryant MP & Small N (1956) Characteristics of two new genera of anaerobic curved rods isolated from the rumen of cattle. J Bacteriol 72: 22-26.
    • (1956) J Bacteriol , vol.72 , pp. 22-26
    • Bryant, M.P.1    Small, N.2
  • 6
    • 77953626492 scopus 로고    scopus 로고
    • Cellulosilyticum ruminicola a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate-borne fibrolytic enzymes
    • Cai SC, Li JB, Hu FZ, Zhang KG, Luo YM, Janto B, Boissy R, Ehrlich G & Dong XZ (2010) Cellulosilyticum ruminicola a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate-borne fibrolytic enzymes. Appl Environ Microbiol 76: 3818-3824.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 3818-3824
    • Cai, S.C.1    Li, J.B.2    Hu, F.Z.3    Zhang, K.G.4    Luo, Y.M.5    Janto, B.6    Boissy, R.7    Ehrlich, G.8    Dong, X.Z.9
  • 7
    • 78649670032 scopus 로고    scopus 로고
    • Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing
    • Callaway TR, Dowd SE, Edrington TS, Anderson RC, Krueger N, Bauer N, Kononoff PL & Nisbet DJ (2010) Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing. J Anim Sci 88: 3977-3983.
    • (2010) J Anim Sci , vol.88 , pp. 3977-3983
    • Callaway, T.R.1    Dowd, S.E.2    Edrington, T.S.3    Anderson, R.C.4    Krueger, N.5    Bauer, N.6    Kononoff, P.L.7    Nisbet, D.J.8
  • 9
    • 0037388225 scopus 로고    scopus 로고
    • Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity
    • 796, 798 passim.
    • Crosby LD & Criddle CS (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34: 790-794, 796, 798 passim.
    • (2003) Biotechniques , vol.34 , pp. 790-794
    • Crosby, L.D.1    Criddle, C.S.2
  • 10
    • 0001463120 scopus 로고
    • Digestibility of forage hemicellulose and pectin by rumen bacteria in vitro and the effect of lignification thereon
    • Dehority BA, Johnson RR & Conrad HR (1962) Digestibility of forage hemicellulose and pectin by rumen bacteria in vitro and the effect of lignification thereon. J Dairy Sci 50: 1136-1141.
    • (1962) J Dairy Sci , vol.50 , pp. 1136-1141
    • Dehority, B.A.1    Johnson, R.R.2    Conrad, H.R.3
  • 11
    • 33751016342 scopus 로고    scopus 로고
    • Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen
    • Denman SE & McSweeney CS (2006) Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiol Ecol 58: 572-582.
    • (2006) FEMS Microbiol Ecol , vol.58 , pp. 572-582
    • Denman, S.E.1    McSweeney, C.S.2
  • 12
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: an approach using the bootstrap
    • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 13
    • 0015296560 scopus 로고
    • Fermentation of isolated pectin and pectin from intact forages by pure cultures of rumen bacteria
    • Gradel CM & Dehority BA (1972) Fermentation of isolated pectin and pectin from intact forages by pure cultures of rumen bacteria. Appl Microbiol 23: 332-340.
    • (1972) Appl Microbiol , vol.23 , pp. 332-340
    • Gradel, C.M.1    Dehority, B.A.2
  • 14
    • 0028834208 scopus 로고
    • Degradation characteristics of isolated and in situ cell wall lucerne pectic polysaccharides by mixed ruminal microbes
    • Hatfield RD & Weimer PJ (1995) Degradation characteristics of isolated and in situ cell wall lucerne pectic polysaccharides by mixed ruminal microbes. J Sci Food Agric 69: 185-196.
    • (1995) J Sci Food Agric , vol.69 , pp. 185-196
    • Hatfield, R.D.1    Weimer, P.J.2
  • 15
    • 0027363920 scopus 로고
    • Polymerase chain reaction detection of nonviable bacterial pathogens
    • Josephson KL, Gerba CP & Pepper IL (1993) Polymerase chain reaction detection of nonviable bacterial pathogens. Appl Environ Microbiol 59: 3513-3515.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 3513-3515
    • Josephson, K.L.1    Gerba, C.P.2    Pepper, I.L.3
  • 16
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 17
    • 0042882236 scopus 로고    scopus 로고
    • Establishing populations of Megasphaera elsdenii YE 34 and Butyrivibrio fibrisolvens YE 44 in the rumen of cattle fed high grain diets
    • Klieve AV, Hennessy D, Ouwerkerk D, Forster RJ, Mackie RI & Attwood GT (2003) Establishing populations of Megasphaera elsdenii YE 34 and Butyrivibrio fibrisolvens YE 44 in the rumen of cattle fed high grain diets. J Appl Microbiol 95: 621-630.
    • (2003) J Appl Microbiol , vol.95 , pp. 621-630
    • Klieve, A.V.1    Hennessy, D.2    Ouwerkerk, D.3    Forster, R.J.4    Mackie, R.I.5    Attwood, G.T.6
  • 18
    • 33847359626 scopus 로고    scopus 로고
    • Validation and application of real-time polymerase chain reaction assays for representative rumen bacteria
    • Koike S, Yabuki H & Kobayashi Y (2007) Validation and application of real-time polymerase chain reaction assays for representative rumen bacteria. Anim Sci J 78: 135-141.
    • (2007) Anim Sci J , vol.78 , pp. 135-141
    • Koike, S.1    Yabuki, H.2    Kobayashi, Y.3
  • 20
    • 44449151076 scopus 로고    scopus 로고
    • Effect of extraction conditions on some physicochemical characteristics of pectins from "Améliorée" and "Mango" mango peels
    • Koubala BB, Kansci G, Mbome LI, Crépeau MJ, Thibault JF & Ralet MC (2008) Effect of extraction conditions on some physicochemical characteristics of pectins from "Améliorée" and "Mango" mango peels. Food Hydrocolloids 22: 1345-1351.
    • (2008) Food Hydrocolloids , vol.22 , pp. 1345-1351
    • Koubala, B.B.1    Kansci, G.2    Mbome, L.I.3    Crépeau, M.J.4    Thibault, J.F.5    Ralet, M.C.6
  • 21
    • 27644437124 scopus 로고
    • The carbohydrates in alfalfa Medicago sativa I. General composition identification of a nonreducing sugar and investigation of the pectic substances
    • Lagowski JM, Sell HM, Huffman CF & Duncan CW (1958) The carbohydrates in alfalfa Medicago sativa I. General composition identification of a nonreducing sugar and investigation of the pectic substances. Arch Biochem Biophys 76: 306-316.
    • (1958) Arch Biochem Biophys , vol.76 , pp. 306-316
    • Lagowski, J.M.1    Sell, H.M.2    Huffman, C.F.3    Duncan, C.W.4
  • 22
    • 84863288435 scopus 로고    scopus 로고
    • Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms
    • Lan Y, Wang Q, Cole JR & Rosen GL (2012) Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms. PLoS One 7: e32491.
    • (2012) PLoS One , vol.7
    • Lan, Y.1    Wang, Q.2    Cole, J.R.3    Rosen, G.L.4
  • 23
    • 84866166160 scopus 로고    scopus 로고
    • Comparative survey of rumen microbial communities and metabolites across one caprine and three bovine groups, using bar-coded pyrosequencing and (1)H nuclear magnetic resonance spectroscopy
    • Lee HJ, Jung JY, Oh YK, Lee SS, Madsen EL & Jeon CO (2012) Comparative survey of rumen microbial communities and metabolites across one caprine and three bovine groups, using bar-coded pyrosequencing and (1)H nuclear magnetic resonance spectroscopy. Appl Environ Microbiol 78: 5983-5993.
    • (2012) Appl Environ Microbiol , vol.78 , pp. 5983-5993
    • Lee, H.J.1    Jung, J.Y.2    Oh, Y.K.3    Lee, S.S.4    Madsen, E.L.5    Jeon, C.O.6
  • 24
    • 84872922866 scopus 로고    scopus 로고
    • In vitro rumen fermentation and methane production are influenced by active components of essential oils combined with fumarate
    • Lin B, Wang JH, Lu Y, Liang Q & Liu JX (2011) In vitro rumen fermentation and methane production are influenced by active components of essential oils combined with fumarate. J Anim Physiol Anim Nutr 97: 1-9.
    • (2011) J Anim Physiol Anim Nutr , vol.97 , pp. 1-9
    • Lin, B.1    Wang, J.H.2    Lu, Y.3    Liang, Q.4    Liu, J.X.5
  • 25
    • 84896700199 scopus 로고    scopus 로고
    • Reinventing alfalfa for dairy cattle and novel uses. California Alfalfa and Forage Symposium, Visalia, CA.
    • Martin NP & Mertens DR (2005) Reinventing alfalfa for dairy cattle and novel uses. California Alfalfa and Forage Symposium, Visalia, CA.
    • (2005)
    • Martin, N.P.1    Mertens, D.R.2
  • 26
    • 84896711749 scopus 로고    scopus 로고
    • Nutritional implications of fiber and carbohydrate characteristics of corn silage and alfalfa hay. California Anim Nutr Conf, Fresno, CA.
    • Mertens DR (2002) Nutritional implications of fiber and carbohydrate characteristics of corn silage and alfalfa hay. California Anim Nutr Conf, Fresno, CA.
    • (2002)
    • Mertens, D.R.1
  • 27
    • 77956095453 scopus 로고    scopus 로고
    • Metagenomic sequencing of an in vitro-simulated microbial community
    • Morgan JL, Darling AE & Eisen JA (2010) Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One 5: e10209.
    • (2010) PLoS One , vol.5
    • Morgan, J.L.1    Darling, A.E.2    Eisen, J.A.3
  • 29
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • Muyzer G, De Waal EC & Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 30
    • 0003702261 scopus 로고    scopus 로고
    • National Research Council, seventh revised edn. National Academy Press, Washington, D.C.
    • National Research Council (2001) Nutrient Requirement of Dairy Cattle, seventh revised edn. National Academy Press, Washington, D.C.
    • (2001) Nutrient Requirement of Dairy Cattle
  • 31
    • 33644965765 scopus 로고    scopus 로고
    • Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide
    • Nocker A & Camper AK (2006) Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide. Appl Environ Microbiol 72: 1997-2004.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 1997-2004
    • Nocker, A.1    Camper, A.K.2
  • 32
    • 0031942287 scopus 로고    scopus 로고
    • Emended description of Campylobacter sputorum and revision of its infrasubspecific (biovar) divisions, including C. sputorum biovar paraureolyticus, a urease-producing variant from cattle and humans
    • On SL, Atabay HI, Corry JE, Harrington CS & Vandamme P (1998) Emended description of Campylobacter sputorum and revision of its infrasubspecific (biovar) divisions, including C. sputorum biovar paraureolyticus, a urease-producing variant from cattle and humans. Int J Syst Bacteriol 48 Pt 1: 195-206.
    • (1998) Int J Syst Bacteriol , vol.48 PART 1 , pp. 195-206
    • On, S.L.1    Atabay, H.I.2    Corry, J.E.3    Harrington, C.S.4    Vandamme, P.5
  • 33
    • 0021846501 scopus 로고
    • Treponema saccharophilum sp. nov., a large pectinolytic spirochete from the bovine rumen
    • Paster BJ & Canale-Parola E (1985) Treponema saccharophilum sp. nov., a large pectinolytic spirochete from the bovine rumen. Appl Environ Microbiol 50: 212-219.
    • (1985) Appl Environ Microbiol , vol.50 , pp. 212-219
    • Paster, B.J.1    Canale-Parola, E.2
  • 34
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • Polz MF & Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 35
    • 0024438993 scopus 로고
    • A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA
    • Rychlik W & Rhoads RE (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res 17: 8543-8551.
    • (1989) Nucleic Acids Res , vol.17 , pp. 8543-8551
    • Rychlik, W.1    Rhoads, R.E.2
  • 36
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N & Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 37
    • 0011818310 scopus 로고    scopus 로고
    • SAS Institute Version 8.01. SAS Inst. Inc., Cary, NC.
    • SAS Institute (2000) SAS User's Guide: Statistics. Version 8.01. SAS Inst. Inc., Cary, NC.
    • (2000) SAS User's Guide: Statistics
  • 38
    • 84867103637 scopus 로고    scopus 로고
    • Insertion depth of oral stomach tubes may affect the fermentation parameters of ruminal fluid collected in dairy cows
    • Shen JS, Chai Z, Song LJ, Liu JX & Wu YM (2012) Insertion depth of oral stomach tubes may affect the fermentation parameters of ruminal fluid collected in dairy cows. J Dairy Sci 95: 5978-5984.
    • (2012) J Dairy Sci , vol.95 , pp. 5978-5984
    • Shen, J.S.1    Chai, Z.2    Song, L.J.3    Liu, J.X.4    Wu, Y.M.5
  • 39
    • 0030980044 scopus 로고    scopus 로고
    • Competition for cellulose among three predominant ruminal cellulolytic bacteria under substrate-excess and substrate-limited conditions
    • Shi Y, Odt CL & Weimer PJ (1997) Competition for cellulose among three predominant ruminal cellulolytic bacteria under substrate-excess and substrate-limited conditions. Appl Environ Microbiol 63: 734-742.
    • (1997) Appl Environ Microbiol , vol.63 , pp. 734-742
    • Shi, Y.1    Odt, C.L.2    Weimer, P.J.3
  • 41
    • 0019166205 scopus 로고
    • Treponema bryantii sp. nov., a rumen spirochete that interacts with cellulolytic bacteria
    • Stanton TB & Canale-Parola E (1980) Treponema bryantii sp. nov., a rumen spirochete that interacts with cellulolytic bacteria. Arch Microbiol 127: 145-156.
    • (1980) Arch Microbiol , vol.127 , pp. 145-156
    • Stanton, T.B.1    Canale-Parola, E.2
  • 42
    • 34247620908 scopus 로고    scopus 로고
    • Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR
    • Stevenson DM & Weimer PJ (2007) Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR. Appl Microbiol Biotechnol 75: 165-174.
    • (2007) Appl Microbiol Biotechnol , vol.75 , pp. 165-174
    • Stevenson, D.M.1    Weimer, P.J.2
  • 44
    • 34547781750 scopus 로고    scopus 로고
    • mega4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0
    • Tamura K, Dudley J, Nei M & Kumar S (2007) mega4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Mol Biol Evol 24: 1596-1599.
    • (2007) Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 45
    • 0000945405 scopus 로고
    • A simple gas production method using a pressure transducer to determine the fermentation kinetics of ruminant feeds
    • Theodorou MK, Williamsa BA, Dhanoaa MS, McAllana AB & Franceb J (1994) A simple gas production method using a pressure transducer to determine the fermentation kinetics of ruminant feeds. Anim Feed Sci Technol 48: 185-197.
    • (1994) Anim Feed Sci Technol , vol.48 , pp. 185-197
    • Theodorou, M.K.1    Williamsa, B.A.2    Dhanoaa, M.S.3    McAllana, A.B.4    Franceb, J.5
  • 46
    • 0027968068 scopus 로고
    • clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG & Gibson TJ (1994) clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 47
    • 0026232176 scopus 로고
    • Symposium: carbohydrate methodology metabolism and nutritional implications in dairy cattle
    • Van Soest PJ, Robertson JB & Lewis BA (1991) Symposium: carbohydrate methodology metabolism and nutritional implications in dairy cattle. J Dairy Sci 74: 3583-3597.
    • (1991) J Dairy Sci , vol.74 , pp. 3583-3597
    • Van Soest, P.J.1    Robertson, J.B.2    Lewis, B.A.3
  • 48
    • 84982343016 scopus 로고
    • The comprehensive analysis of grasses
    • Waite R & Gorrod ARN (1959) The comprehensive analysis of grasses. J Sci Food Agric 10: 317-326.
    • (1959) J Sci Food Agric , vol.10 , pp. 317-326
    • Waite, R.1    Gorrod, A.R.N.2
  • 49
    • 2442510059 scopus 로고    scopus 로고
    • Improved extraction of PCR-quality community DNA from digesta and fecal samples
    • Yu Z & Morrison M (2004) Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36: 808-812.
    • (2004) Biotechniques , vol.36 , pp. 808-812
    • Yu, Z.1    Morrison, M.2
  • 51
    • 84874294859 scopus 로고    scopus 로고
    • Effects of dietary forage sources on rumen microbial protein synthesis and milk performance in early lactating dairy cows
    • Zhu W, Fu Y, Wang B, Wang C, Ye JA, Wu YM & Liu JX (2013) Effects of dietary forage sources on rumen microbial protein synthesis and milk performance in early lactating dairy cows. J Dairy Sci 96: 1727-1734.
    • (2013) J Dairy Sci , vol.96 , pp. 1727-1734
    • Zhu, W.1    Fu, Y.2    Wang, B.3    Wang, C.4    Ye, J.A.5    Wu, Y.M.6    Liu, J.X.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.